Meet Our Recent Alumni
Meet Our Recent Alumni
Christian Adams
B.S., CHEMISTRY-BIOCHEMISTRY
FORT LEWIS COLLEGE
Defended August 2006. Currently a Postdoc at Stanford University.
Single Molecule and Biochemical Investigations of Tn5 Transposase DNA Interactions
The Tn5 transposon is a prokaryotic transposition system that uses only three macromolecular components to complete its transposition reaction. These modules are: 1) the transposase, 2) the 19 base pair recognition sequences that are recognized by the transposase and, 3) target DNA. The versatility of the system lies in the fact that any DNA sequence can be placed between the two recognition sequences, allowing for the delivery of any genetic material into the genome of an appropriate organism via the Tn5 system.
In addition to being a useful biotechnological tool, Tn5 provides me with means to study protein-DNA interactions. The transposase has specific recognition sequences, yet also has a significant non-specific DNA binding activity. These two modes of binding allow for a variety of experiments investigating the mechanisms the transposase uses to interact with DNA.
My work has focused on studying the protein DNA interactions of the transposase using two different experimental systems. Using biochemical and molecular biological techniques, I have investigated an alternate mode of binding and dimerization used by the transposase and found that it may represent a mechanism for inhibition of the transposition reactions. I am currently studying Tn5 transposition at the single molecule level in collaboration with a group in Chicago. In these experiments I use long molecules of DNA tethered to magnetic beads to study the interactions of the transposase with both non-specific and specific DNA. It has been exciting to work with two groups, one in Madison using the tools of biochemistry and molecular biology to study Tn5, and one in Chicago where I am in the middle of the development of a new field, the study of protein DNA interactions at the single molecule level.
The Biochemistry Department at the University of Wisconsin at Madison was an excellent choice for me. The size and scientific diversity of the department allowed me to completely explore my interests before joining a lab. The department has a very strong support system for graduate students so that I felt welcome and at home from the first day I walked in the building. I have made life-long friends with many of my classmates.
Madison is a wonderful place to live. The city is very civic-minded, with active, thoughtful citizens and a culture that values social awareness, health and intellectual pursuits. There are numerous activities to be found within the city limits: running out to Picnic Point, dining out on the Capitol Square or the East Side, music at the Terrace, hiking in the Arboretum, cross-country skiing on Lake Mendota, mountain biking at the Quarryxand enjoying the sunset and beer with friends at the University’s Memorial Union Terrace are just a few of the ways I have enjoyed myself here in Madison. The city of Madison and the Department of Biochemistry are vibrant and exciting places to live life and do science.
Alison Albee
B.S., MOLECULAR BIOLOGY
PURDUE UNIVERSITY
Defended August 2008. Currently a Postdoc at Washington University.
TACCt at UW-Madison
Transforming acidic coiled coil (TACC) proteins are conserved in a wide range of species from yeast to humans. They have been shown to be centrosomal proteins and involved in mitotic spindle assembly. The mitotic spindle is an elaborate macromolecular machine devised by the cell to ensure that the chromosomes are equally segregated during mitosis. Mitotic spindle assembly is an important step in mitosis and errors in the spindle can lead to cell cycle arrest, mis-segregation of chromosomes, and genomic instability, which in turn leads to serious human diseases including developmental defects and cancer. I am interested in the role of the Xenopus TACC homolog, maskin, in spindle assembly.
What first attracted me to the biochemistry department at the University of Wisconsin-Madison was its excellent reputation and exciting science. What kept me here was the city of Madison. The city and university are a perfect complement to each other. The environment has been ideal for personal and professional growth. I have learned to think in a new way and how to better approach problems. I have also had the opportunity to try new activities I never thought I would before, such as skydiving, caving, and mechanical bullriding. Whatever your choice may be, I can’t recommend the University of Wisconsin-Madison enough. In addition to the excellent research opportunities the department has to offer, it also has the bonus of being dangerously close to Babcock Hall, famous for their ice cream. On summer afternoons, there is a steady stream of people from the biochemistry building to Babcock for ice cream!
Daniel Blasiole
B.A., PHILOSOPHY,
FRANKLIN AND MARSHALL COLLEGE
M.A., PHILOSOPHY,
UNIVERSITY OF CALIFORNIA, SAN DIEGO
Defended March 2008. Currently a Patent Technical Advisor at a law firm in Madison.
Cutting-edge science in a great place to call home
I work on uncovering molecular processes by which the liver regulates plasma lipid homeostasis. The liver plays a major role in controlling plasma lipid levels by both secreting and clearing lipoproteins. It has long been known that the hepatic clearance of LDL and other lipoproteins is largely mediated the LDL receptor. The Attie laboratory discovered a novel role of the LDL receptor in that it also regulates lipoprotein secretion. I use cellular and molecular techniques to investigate how the receptor carries out this function. In addition to studying the LDL receptor directly, I also study the mechanism by which a newly discovered proprotein convertase, PCSK9, promotes the degradation of the LDL receptor. By lowering LDL receptor activity in the liver, mutations in PCSK9 lead to clinical hypercholesterolemia in humans. It is exciting to work in a field in which specific biochemical questions have clinical implications.
I entered graduate school with the aim of studying molecular mechanisms underlying human disease, particularly in the areas of lipid and carbohydrate metabolism. The Department of Biochemistry offers several opportunities for collaboration with renowned researchers within my specific field. In addition, the wide-ranging interests within the department, as well as throughout the UW, provide many opportunities for exploring areas of research with experts outside my specialty.
As a married graduate student with two children (and coming from San Diego), I have found Madison the perfect place to live. It has a balanced mix of big-city amenities with a small-town feel. Any given day in Madison might include cycling in the beautiful Dane County countryside, kayaking in the surrounding lakes and rivers, listening to live music on the shore of Lake Mendota, touring one of the many art museums, or shopping for locally grown vegetables at a farmer’s market. Unlike most cities in the U.S., all of Madison’s amenities are accessible by an extensive network of bike paths, most of which are plowed in the winter!
Graduate school in Biochemistry at UW offers cutting-edge science in great place to call home.
Laurieann Casey
B.S., BIOCHEMISTRY
WASHINGTON UNIVERSITY
Defended May 2007. Currently a Postdoc at Albany Medical College.
Not in a million years did I imagine myself living in Wisconsin, much less falling in love with my life here in the dairy state. Although I intended to attend graduate school on one of the coasts, I applied to the University of Wisconsin- Madison because my undergraduate advisor would not stop singing its praises until I did so. Ranked among the top ten graduate schools for biochemical sciences and among the top ten public universities for receipt of federal research funds, the University of Wisconsin- Madison met my criteria for being a renowned research institution. Upon visiting during the interview process, I was impressed by the collegiality among the faculty and closeness and friendly interactions between the faculty and students. The professors take their mission to teach and train graduate students seriously and truly devote themselves to the development and success of their students. Their passion for science is infectious. A daily coffee station outside the department office and a social beer hour following the weekly seminars encourage the spontaneous exchange of ideas and solutions to problems. I decided this intimate supportive atmosphere would be the best training environment.
In addition, the university offers outstanding centralized facilities such as those in the Biotechnology and Genome Center. My own project has focused on understanding the complex connections between an evolutionarily conserved transcription factor, the cell cycle and the assembly of specialized chromatin and I have had to use biochemical, genetic and cell biological approaches. Through hard work and certainly some set-backs I have made some exciting new discoveries that have been advanced in part because of the wonderful interactions and collaborative intellectual environment at Madison. Labs from various departments working in similar fields gather weekly or monthly to present and discuss their research and each department hosts a variety of outside speakers offering ample opportunities to learn about a variety of topics and to meet prominent scientists from other research fields.
I recall during my first visit to the university how happy the students were. After living in Madison, I can see why. Being the capitol and home to its largest state university the city offers many cultural experiences, diverse ethnic restaurants and music venues and festivals. At the same time, the small size of the city makes it safe and keeps it traffic-free. The cost of living is affordable and allows graduate students to lead comfortable lives. Personally, I have taken advantage of Madison’s outdoor activities. I learned to rock climb in a nearby state park, to white water kayak through a club on campus, and play ultimate Frisbee, softball, and soccer on various city and intramural leagues. An extensive bike path system allows easy transportation for those without a car. Finally, the Madison environment allows graduate students to maintain a balance between intense research training and a life outside the lab.
Jackie Fretz
B.S., BIOCHEMISTRY
UNIVERSITY OF NEW HAMPSHIRE
Defended August 2007. Currently a Postdoc at Yale Medical School.
Exploring theTranscriptional Activities of
NFATc1 in Osteoclasts
In bone, homeostasis is maintained through the coordinated actions of the matrix building osteoblast and the mineral resorbing osteoclast. In disease states, these opposing actions become uncoupled. Although the cytokine responsible for stimulating osteoclast differentiation has been identified, we still understand very little about the signaling events necessary for maturation, multinucleation, and activation of these unique cells. My research has been focused on elucidating the mechanisms by which NFATc1 controls gene expression during osteoclast differentiation. To this end, we investigate how NFATc1 participates in the regulation of multiple target genes previously identified as important to osteoclast differentiation, identify novel targets of NFATc1 regulation, and evaluate how the cooperative or inhibitory interactions of other transcription factors and signaling pathways modulate the activity of NFATc1.
I chose the graduate program in Biochemistry at the University of Wisconsin not only for the high rankings of the program and nationally and internationally recognized faculty, but also because of the unique character of Madison. When asking several professors at my undergraduate program what they thought of the University of Wisconsin the unanimous reaction was “Madison! I love Madison!” and after one visit I had to agree. The city uniquely combines the cultural and entertainment scene of a large metropolis while avoiding the congestion and “concrete jungle” trappings of other locations. I love taking in a show at the Overture Center for the Arts, Comedy Club, or Dane County Coliseum, as well as trying new cuisine at the multitude of the restaurants which highlight food from all over the world. At the same time, I go home at night to a quiet neighborhood and a large yard, ride to work on community bike trails, feel safe coming into lab at all hours of the day or night, and escape on the weekends to the nearby state parks.
For the Biochemistry Department itself, I could not have had the chance to work with a more engaging, fun, or personable group of students. There is a real sense of community fostered within members of each incoming class and among students at all levels of their graduate career. Throughout the year, there are a multitude of social events sponsored by the Student Faculty Liaison Committee (SFLC) which reinforce these ties and provide opportunities to catch up with other students who you may not have had the opportunity to connect on a more regular basis. I have met many people with whom I believe I will share life-long friendships, and who I will sincerely miss when my husband and I move on to the next stage of our lives.
Michael Guy
B.S., CHEMISTRY
UTAH STATE UNIVERSITY
Defended August 2008. Currently a Postdoc at Mayo Clinic.
Apoptotis, P49, and Family Life
Apoptosis is a cell suicide pathway that is highly conserved from worms to humans and is crucial in development, prevention of cancer, and as an anti-viral defense. I am interested in the cellular processes involved in apoptosis, in particular the proteolytic caspase cascade. Using site-directed mutagenesis, recombinant viruses, in vitro assays, and other biochemical approaches, I am studying how baculovirus P49 blocks apoptosis. Understanding how this novel viral protein inhibits caspases will give unique insight into caspase activation and regulation.
The faculty and students of the Biochemistry Department have a wide variety of research interests and are very congenial and collaborative. I am always impressed with the high quality of research achieved in the department as well. In addition to the great research and academic atmosphere, UW-Madison is a fun place to go to school. Whether playing in the intramural basketball leagues, watching the Badger football team at Camp Randall stadium, or enjoying some famous Babcock Dairy ice cream, I’ve found plenty to do in addition to research. And if you happen to get hurt (doing research or something else like playing basketball), the health care is great and covers anything from knee surgery to having a baby. Trust me, my wife and I know!
I am married (Adrian) and have two children (Rebecca and Scott). Madison has been a great place to raise a family. In addition to the nice people here in Madison, there are free concerts, a great parks and recreation system, a free zoo, beautiful lakes, and other wonderful things to see and do in the outlying country. We love living here in Madison.
Byung Woo Han
B.S., CHEMISTRY EDUCATION
M.S., CHEMISTRY
SEOUL NATIONAL UNIVERSITY, KOREA
Defended May 2006. Currently a Postdoc at Scripps Research Institute.
Structure determination of calmodulin-related proteins in Arabidopsis thaliana by x-ray crystallography
Calmodulin is one of the representative calcium sensors in plants and animals. In plants, there are more than ten calmodulin isoforms, putative calmodulins and calcium dependent protein kinases with a calmodulin-like domain. There are only a couple of calmodulins in animals. My research project is to determine the three dimensional structures of the proteins which contain a calmodulin-like domain by X-ray crystallography to elucidate the diverse calcium signal transduction mechanism in plants. Structural biology in the Department of Biochemistry at UW-Madison is getting stronger thanks to the Center for Eukaryotic Structural Genomics (CESG) and the National Magnetic Resonance Facility at Madison (NMRFAM).
I started horseback riding through the UW Hoofers Program two years ago. I never rode a horse before I came to Madison. I go to the Hoofers Equestrian Center once a week to enjoy this pleasant outdoor activity. Madison is such a wonderful place for other outdoor activities, such as running, hiking, sailing, and biking. Since my arrival in Madison in the fall of 2001, now I consider Madison as my second hometown. I feel as comfortable as I do in my original hometown, the Chiak Mountain in Korea.
Michael Hobbs
B.S., CHEMISTRY
UNIVERSITY OF LOUISVILLE
Defended August 2006. Currently a Scientist with Invitrogen in Madison.
Equity and Enzymology, who could ask for anything more
Understanding the biochemical reactions, which when summed, yield a living organism is certainly an exciting way to spend one’s life. Harnessing this personal drive to make scientific progress, through clear thinking, sound laboratory practice and elegant experimental design, is what graduate school should be about. The focus placed on the formation of quality scientists in our department ranks very high among my reasons for choosing Biochemistry at UW-Madison. We are a department as committed to producing future colleagues as we are to contributing ground-breaking discoveries.
Scientifically, I am interested in the mechanism by which proteins bind DNA non-specifically. The enzymes catalyzing recombinational DNA repair rely on this class of interaction, as DNA damage is not restricted to specific DNA sequences. In the Cox Lab, we study recombinational DNA repair in both Escherichia coli and Deinococcus radiodurans. In these bacterial organisms, repair of damaged DNA is largely dependent upon the RecA protein to catalyze recombination events. My project centers around the recombination mediator proteins RecFOR, which direct the binding of RecA to single-stranded DNA under certain conditions.
My project has been difficult, but extremely rewarding. It draws widely upon my background knowledge in fields as disparate as mathematical topology and biophysical chemistry. My training is concentrated on learning to synthesize new theories from what is already known. This is the central skill of the scientist, and I am proud of how I’ve developed professionally at UW.
Madison has been a great place to grow personally as well. While here, I’ve been able to maintain many hobbies, while accruing sailing and home improvement skills (our first home!). My wife enjoys the area very much as well and is steadily advancing her teaching career. We’ve found Madison to be a very hospitable, diverse, and safe community. The fine arts are well-represented and the free Vilas Zoo and Olbrich Botanical Gardens certainly provide for the cultural development of young people like ourselves.
The UW is outstanding among Universities; Madison is likewise notable among cities. Working, living, and learning here have been opportunities I will always cherish. I encourage anyone thinking of doing his or her Ph.D. to apply to UW-Madison without reservation.
Kara Lake
B.S., CHEMISTRY, B.S., BIOLOGY
BUTLER UNIVERSITY
Defended June 2007. Currently a Postdoc at UCSF.
What is the mechanism by which synaptotagmin regulates neurosecretion?
The release of neurotransmitters from neurons and hormones from neuroendocrine cells occurs through exocytosis of secretory vesicles. This transmission takes place on a millisecond time scale and relies on calcium-triggered fusion of secretory vesicles with the plasma membrane. The mechanism for calcium-triggered fusion remains unclear. Current findings suggest that synaptotagmin proteins are the molecular means by which calcium regulates membrane fusion. My research focuses on determining the functional role of synaptotagmin in exocytosis and investigating the biochemical properties responsible for its mechanism of regulation.
I continue to be thankful that I decided to come to the UW-Madison Biochemistry Department for graduate school. The high level of research conducted here is made possible by the supportive environment fostered by other students and professors. Besides a wonderful biochemistry department, Madison and the University of Wisconsin have a lot to offer. I am not only able to pursue my interests in Biochemistry, but also my interests outside of science. At different points throughout my time here, I have been able to take advantage of the multiple opportunities that are available. Through such things as playing on a Biochemistry softball team, getting involved in Intervarsity Graduate Christian Fellowship, playing intramural soccer, assistant coaching a high school girls cross-country and track team, attending UW home football games with other Biochemistry students, snowboarding with friends and enjoying the lively environment of Madison, I continue to grow here as a well-rounded person and scientist.
Liana Lamont
B.S, BIOCHEMISTRY
UNIVERSITY OF ILLINOIS, URBANA-CHAMPAIGN
Defended August 2006. Currently a Lecturer for General Chemistry 103, UW Chemistry Department, and Assistant Editor, Journal of Chemical Education.
Regulation of germline development in the nematode Caenorhabditis elegans
Our lab studies the regulation of animal development at the molecular level. We are interested in controls of cell fate and patterning within multi-cellular tissues. The model organism C. elegans enables the identification and analysis of developmental regulators that are used throughout the animal kingdom. My project focuses on how germline stem cells are controlled by the GLP-1 (Notch) signaling pathway. I have taken a multi-faceted approach to identify genes that act downstream of GLP-1 in germline development. I use a combination of biochemical, genetic, and molecular biological techniques to elucidate the role and regulation of candidate genes.
Madison is a fantastic place to be a graduate student. Madison offers the perfect balance — a strong academic community and multiple opportunities to enjoy life outside of lab. The physical space of our departmental building is open to encourage collaboration and facilitate idea sharing. Furthermore, all of the labs on campus that use C. elegans as a model for their studies meet bi-weekly to discuss our current work and exchange technical advice. In addition, Madison offers many fun things to do. The lakes provide a peaceful space to relax, and there are many bike and hiking trails to enjoy around town. To release stress, I play indoor and outdoor soccer. I also enjoy going to concerts and plays at the Madison Civic Center and attending Big Ten sporting events. So far, my four years in Madison have been great. It’s going to be hard to move on to the next challenges wherever I continue my studies.
Mark Meyer
B.S., CHEMISTRY
BUTLER UNIVERSITY
Defended August 2007. Currently a Postdoc in Wes Pike’s Lab.
RXR transactivation and p160 family coactivator regulation in 1,25(OH)2D3 mediated transcription
Vitamin D, discovered here at UW-Madison, is vital for many processes in the body. The active hormonal form of Vitamin D, 1α,25dihydroxy vitamin D3 (1,25D3), acts via the Vitamin D Receptor (VDR). VDR, when bound with 1,25D3, heterodimerizes with and transactivates the retinoid X receptor or RXR. These proteins bind to DNA through specific vitamin D response elements in promoter regions of target genes. To further facilitate transcription initiation, coactivator proteins are recruited. These coactivators, such as SRC/p160 family and CBP, attach VDR/RXR to the basal transcription machinery and RNA polymerase II. Target genes of vitamin D are very diverse and are found in many tissue and cell types. Specifically, our lab and my research are focused on the actions of 1,25D3 in two of the major target tissues, bone and intestine. Through these tissues, serum calcium can be tightly regulated by calcium channels and bone mineralization. I work to further elucidate mechanisms by which RXR is being transactivated and the recruitment of coactivator proteins integral to these processes.
Choosing a graduate program in Biochemistry can be difficult. My decision was made very easy with one visit to the city of Madison and the campus here at the University of Wisconsin. The prestige, national merit, leading professors, and rich history are a few things that make this department the best in the nation. Interdepartmental collaboration with other highly ranked departments here allows for extensive research possibilities.
In life beyond lab, the campus and city are alive with activity and culture. The lakes allow for sailing in the summer and hockey and ice fishing in the winter. There are great winding country roads to bike on, trails for mountain biking and hiking, state parks for camping, and hills for skiing or snowboarding. UW-Madison teams are all nationally ranked and students, yes even graduate students, can easily get tickets for any major sport. For the fine arts, Madison recently completed a new Overture Center which will house the Madison Chamber Orchestra and include a theatre for traveling Broadway plays. With all this and more, it is no wonder that people never want to leave Madison, WI.
Tazeh Ngii
B.S., BIOCHEMISTRY
UNIVERSITY OF BUEA, CAMEROON
Defended December 2007. Currently in Medical School at the University of Iowa.
I made a good decision when I chose to leave the warm and nice tropical weather of Cameroon to move to Madison, Wisconsin for graduate studies. A high school classmate and close friend of mine who at the time was a laboratory assistant in one of the labs in the UW Medical School recommended UW-Madison to me. One of the first things that struck me was how warmhearted the people were; the cordiality of the staff and the welcoming attitude of the students and faculty helped ease the impact of the culture shock I experienced during the first couple of months I was here. The camaraderie that exists between the students and also between the students and the faculty has really been beneficial in my gradual development to becoming a scientist.
The people at the International Student Services were (and still are) a very good resource with all the questions and issues I had about immigration. They have programs like the Madison Friends of International Students and Bridge that help international students transition into the Madison community very smoothly.
Fred Porter
B.S., BIOCHEMISTRY, RUTGERS UNIVERSITY
M.S., MICROBIOLOGY, SETON HALL UNIVERSITY
Defended August 2008. Currently a Postdoc in Yoshihiro Kawaoka’s Lab, UW-Madison School of Veterinary Medicine.
The biological role of the cardiovirus leader protein
I am interested in the molecular biology of picornaviruses, specifically how virally encoded proteins direct host machinery to efficient synthesis of progeny viruses. My research is focused on characterizing the function of the leader protein encoded by the cardiovirus group of picornaviruses. Previous work has shown that this novel protein is phosphorylated and may interact with the internal ribosomal entry site (IRES) in the cardioviral genomic RNA. I am using molecular biology techniques, biochemical assays, and immunological methods to elucidate the role of this protein in cardiovirus infection.
UW-Madison provides me with a first-class environment to pursue graduate study and my research interests. The Biochemistry graduate curriculum has rounded out my training in biochemistry fundamentals while allowing me to choose specific coursework to compliment my research interests. In addition to a dynamic Biochemistry Department, the University is home to the Institute for Molecular Virology – a thriving, interdepartmental community of virology students and faculty who are an asset to my research training.
Madison is a fun city to live in. When I’m not in the lab, I enjoy canoeing the lakes and rivers in and around Madison or bicycling the miles of scenic bike paths. I’ve also visited a few of Madison’s many live music venues that cater to a wide variety of musical tastes. Overall, I believe UW-Madison has unique qualities that would be difficult to find in another graduate school.
Phil Raess
B.S., CHEMISTRY
INDIANA UNIVERSITY
Defended August 2007. Currently beginning his 4th Year of Medical School.
A novel role for cholecystokinin in β-cell growth and survival
Our lab studies the molecular genetics
of type 2 diabetes. Although most people with type 2 diabetes are obese, only a minority of obese people develop type 2 diabetes. We can replicate this dichotomy by studying two different strains of mice that are either diabetes-susceptible or diabetes-resistant when made obese. Our lab uses mouse genetics combined with transcriptional and metabolic profiling to identify genes and pathways that confer resistance or susceptibility to type 2 diabetes. My project is focused on the potential role of cholecystokinin as a mediator of diabetes resistance. We identified CCK by performing microarray analysis of pancreatic islets of obese mice.
As a student in the UW Medical Scientist Training Program (MSTP or MD/PhD program), the first two years of study consist of medical school coursework and laboratory rotations. I was attracted to Biochemistry for my lab rotations by the amount of interesting and clinically relevant research taking place within the department. During my rotation in the Attie lab, I knew I had found my thesis lab. After defending my thesis and completing the PhD portion of my education, I will return to medical school to complete my clinical rotations.
I also enjoy spending time outside of lab. Madison has a nice mix of activities – summertime means hanging out at the Union Terrace on the shores of Lake Mendota, watching sailboats and windsurfers as the sun sets. There are frequent outdoor concerts all over town ranging from bluegrass to classical and everything in between. Winter also brings a lot of fun outdoor activities – there are three ski areas within an hour of Madison and lots of opportunities in town to cross-country ski or play ice hockey at local parks. Madison is a wonderful place to train and live, and I will miss it when I move forward with my career.
Bryan Smith
B.S., BIOCHEMISTRY
UNIVERSITY OF NEBRASKA-LINCOLN
Defended May 2006. Currently a Senior Scientist at Deciphera Pharmaceuticals in Lawrence, Kansas.
Discovery, design, and application of ribonuclease inhibitors
Intact RNA and DNA are of central importance to biochemical research and biotechnology. The preservation of these nucleic acids requires the absence of nuclease activity. Ribonucleases are perhaps the most problematic of nucleases because of their high natural abundance, prodigious catalytic activity, notorious conformational stability and resistance to proteolysis, and lack of requisite cofactors. In one of many diverse research projects in the Raines laboratory, we are working on the discovery and development of potent new ribonuclease inhibitors. We study the biophysics and biochemistry of the inhibitors, as well as their biotechnological applications. Ribonuclease inhibitors may also have utility in vivo. Several human ribonucleases are involved in disease, including angiogenin, a ribonuclease that is involved in the growth of new blood vessels in tumors.
The University of Wisconsin-Madison Biochemistry Department is an excellent choice for graduate school. The department is relatively laid back and we have a good deal of freedom to develop new research projects. There are lots of high quality and groundbreaking research projects here, but despite that, the environment is not overly competitive. Whether you are interested in teaching and/or research in academia or working in industry, there are programs and funding to help build your career. For example, I am doing an internship at Invitrogen as part of the Biotechnology Training Program. I hope to start my own biotechnology company some day.
Madison is a great city. My wife and I bought a house (something that would not be possible on the East or West coast) and we enjoy gardening, entertaining, and the many other joys of home ownership. There are great college sports teams here and lots of intramural sports and activities to get involved in during all four seasons. There are excellent restaurants and bars near and even on campus. After work, it is really fun to hang out with friends and drink a beer on the Memorial Union Terrace overlooking Lake Mendota.
Christopher Warren
B.S., BIOCHEMISTRY
NORTHWESTERN UNIVERSITY
Defended April 2008. Currently a Postdoc in Aseem Ansari’s Lab.
Determining the Complete Sequence-Specificity of DNA-Binding Molecules by Cognate Site Identity (CSI) Microarrays
Determining the sequence-recognition properties of DNA-binding proteins and small molecules is a major challenge. To address this need, our lab has developed a high-throughput approach that provides a comprehensive profile of the binding properties of DNA-binding molecules. The approach is based on displaying every permutation of a duplex DNA sequence (up to 11 positional variants) on a microarray. The entire sequence space is interrogated simultaneously, and the affinity of a DNA-binding molecule for every sequence is obtained in a rapid, unbiased, and unsupervised manner. Using this platform, we have determined the full molecular recognition profile of numerous engineered small molecules and eukaryotic transcription factors. The approach has also yielded unique insights into the altered sequence-recognition landscapes as a result of cooperative assembly of DNA-binding molecules in a ternary complex.
The University of Wisconsin-Madison has been a perfect place to develop this technique since this is the home of the inventors of the NimbleGen maskless microarray synthesizer, a technology which has been critical to our early successes. But even more vital to our accomplishments is the interdisciplinary spirit of this university. In our lab alone, we have a biochemist, chemist, engineer, bioinformaticist, geneticist, and molecular biologist all working side-by-side. It is this cooperation that keeps UW-Madison such a high ranking school in so many disciplines. And, of course, I can’t neglect mentioning how much fun Madison can be, whether it’s having drinks out on the terrace or playing weekly kickball or dodgeball games.